X-RAY DIFFRACTION Experimental Data & Validation


X-ray Experimental Help

Crystallization

Crystalization Experiments
Method Vapor Diffusion Hanging Drop
pH 7.8
Temperature 291.0
Details 50 mM Tris 1.6 M Natrium Citrate

Crystal Data

Unit Cell
Length (Å) Angle (°)
a = 41.91 α = 90
b = 41.04 β = 104.31
c = 71.52 γ = 90
Symmetry
Space Group P 1 21 1

Diffraction

Diffraction Experiment
ID # Data Collection Temperature
1 100
Diffraction Detector
Detector Diffraction Type Details Collection Date
PIXEL DECTRIS PILATUS 6M -- 2014-12-19
Diffraction Radiation
Monochromator Protocol
-- SINGLE WAVELENGTH
Diffraction Detector Source
Source Type Wavelength List Synchrotron Site Beamline
SYNCHROTRON BESSY BEAMLINE 14.1 0.91841 BESSY 14.1

Data Collection

Overall
Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) R Sym I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot
1.25 40.61 93.0 0.042 -- -- 2.064 -- 61012 -- -3.0 18.262
High Resolution Shell
Resolution (High) Resolution (Low) Percent Possible (All) R Merge I (Observed) R-Sym I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All)
1.25 1.32 90.1 0.248 -- 2.21 1.865 --

Refinement

Statistics
Structure Solution Method Refinement High Resolution Refinement Low Resolution Cut-off Sigma (I) Cut-off Sigma (F) Number of Reflections (All) Number of Reflections (Observed) Number of Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work R-Free R-Free Selection Details
FOURIER SYNTHESIS 1.25 40.61 -- 0.0 -- 60006 1001 93.11 -- 0.1287 0.1282 0.1623 RANDOM
High Resolution Shell
Refinement method Shell Resolution (High) Shell Resolution (Low) # of Reflections (Observed) # of Reflections (R-Free) # of Reflections (R-Work) R-Factor (R-Work) R-Factor (R-Free) R-Factor (R-Free Error) Percent Reflections (Observed)
X Ray Diffraction 1.249 1.281 -- 65 3923 0.227 0.264 0.0 83.19
Temperature Factor Modeling
Temperature Factor Value
Mean Isotropic B 17.478
Anisotropic B[1][1] 0.14
Anisotropic B[1][2] 0.0
Anisotropic B[1][3] 0.09
Anisotropic B[2][2] -0.92
Anisotropic B[2][3] 0.0
Anisotropic B[3][3] 0.65
RMS Deviations
Key Refinement Restraint Deviation
r_sphericity_free 29.887
r_gen_planes_other 0.005
r_dihedral_angle_3_deg 11.248
r_gen_planes_refined 0.011
r_angle_refined_deg 1.721
r_dihedral_angle_1_deg 6.892
r_dihedral_angle_2_deg 34.79
r_sphericity_bonded 9.574
r_chiral_restr 0.099
r_dihedral_angle_4_deg 20.519
r_rigid_bond_restr 4.207
r_bond_refined_d 0.013
r_angle_other_deg 1.166
r_bond_other_d 0.004
Number of Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms Numbers
Protein Atoms 2019
Nucleic Acid Atoms 0
Heterogen Atoms 36
Solvent Atoms 285

Software

Software
Software Name Purpose
XSCALE data scaling
REFMAC refinement version: refmac_5.8.0103
PDB_EXTRACT data extraction version: 3.22
XDS data reduction